| Glycine Willd. is made up of Subgenus Glycine and Subgenus Soja. Subgenus Soja contains cultivated soybean (Glycine max (L.) Merr.) and annual wild soybean (Glycine soja Sieb. & Zucc.). Wild soybean belongs to herbaceous plants with twining, procumbent, prostrate stem, and its seed size is below 3 g in 100-seed weight. A big seed type above 3 g 100-seed weight is often found in the natural wild soybean populations, and its morphological characters were between wild and cultivated soybean. The former Soviet Union scholar Skvortzow (1927) defined this plant as G. gracilis. With regard to the origin of semi-wild soybean, some scholars think it is the hybridization progeny between wild and cultivated soybeans, while others consider it as an evolutionary transitional type from wild to cultivated soybean.The National Genebank has preserved about 6000 wild soybean accessions, including more than over 1400 semi-wild soybean accessions. The semi-wild soybean is the most abundant in morphology, with many seed colors (black, brown, yellow, green, bicolor, and various mixed color) and stem forms (twining, procumbent, rampant, semi-rampant, semi-erect and erect).Semi-wild soybean overlaps with cultivated soybeans in 100-seed weight, and with wild soybean and cultivated soybean in stem form. However, semi-wild soybean has still been retained inconsistent in its taxonomic belongingness between the other two species. Study on the genetic diversity of semi-wild soybean has significant value for tracing origin, evolution, and classification of soybean.This research is conducted with 20 pairs of SSR primers using 858 accessions of wild, semi-wild, and cultivated soybean. The genetic divergence in different seed weights and seed-coat colors and taxonomic assignment of semi-wild soybean was analyzed within the subgenus Soja. The genetic diversity of wild and semi-wild soybeans from various eco-regions in China was also evaluated. The results were as follows:1. In this research, we evaluated the genetic differentiation in the subgenus Soja and determined the assignment of semi-wild soybean using 421 accessions of wild (two groups), semi-wild (three groups) and"Moshidou"-type soybean landrace (one group). The results showed that semi-wild soybean is an intraspecies variant of wild soybean but not of cultivated soybeans. The 100-seed weight showed genetic evidence that seed size could be used as an index of evolutionary degree in the subgenus Soja.2. Further study on the genetic differentiation within the subgenus Soja in the aspects of different seed weights and seed colors showed that the genetic diversity of wild and semi-wild soybean is obviously higher than cultivated soybean. In the domestication process of cultivated soybean, there may be loss of alleles. The statistic analysis of the rare alleles demonstrated that they were distributed unevenly among different seed colored type although the types were the same seed weights and, which maybe was related to the genetic divergence in different seed colors. The cluster analysis showed basically the same seed color groups gathered together, however, some different seed color groups were divided into different subclusters despite the same seed weights. This indicated that there is genetic divergence between seed colors to some extent. 3. The comparison of genetic diversity in wild soybean among various eco-regions of China showed that the Northeast had the highest genetic diversity, followed by Changjiang Valley, and the Huanghe Valley and Huang-Huai-Hai Valleys were lower. The cluster analysis indicated there was certain association between the genetic structure of wild soybean accessions and geographic distribution.
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